(Cyanato-κN){1-[(E)-phen­yl(pyridin-2-yl-κN)methyl­idene]semicarbazidato-κ2N1,O}copper(II)

Kunnath, R.J.; Prathapachandra Kurup, M.R.; Ng, S.W.

doi:10.1107/S1600536812035386

(Cyanato-κN){1-[(E)-phenyl(pyridin-2-yl-κN)methylidene]semicarbazidato-κ²N¹,O}copper(II)

R. J. Kunnath, M. R. Prathapachandra Kurup and S. W. Ng

The Cu^II atom in the title compound, [Cu(C₁₃H₁₁N₄O)(NCO)], is N,N′,O-chelated by the mono-deprotonated Schiff base ligand and it is also covalently bonded to the nitrogen end of the cyanate ion. The Cu^II atom shows a square-planar coordination that is distorted towards square-pyramidal owing to an intermolecular Cu

N_cyanate interaction [2.623 (2) Å], which gives a centrosymmetric dimer. In the square-planar description, the Cu^II atom is displaced out of the square plane [r.m.s. deviation = 0.048 Å] by 0.084 (1) Å in the direction of the apical occupant. In the crystal, adjacent complex dimers are linked by an amine N—H

N hydrogen-bond pair, also giving a centrosymmetric cyclic association [graph set R₂²(8)], generating a linear chain parallel to [110].

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536812035386/zs2226sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536812035386/zs2226Isup2.hkl Contains datablock I

CCDC reference: 899587

checkCIF report

Key indicators

Single-crystal X-ray study
T = 293 K
Mean (C-C) = 0.003 Å
R factor = 0.029
wR factor = 0.093
Data-to-parameter ratio = 14.8

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT230_ALERT_2_B Hirshfeld Test Diff for    O2     --  C14     ..        7.9 su
PLAT230_ALERT_2_B Hirshfeld Test Diff for    N5     --  C14     ..        7.2 su

Alert level C
PLAT420_ALERT_2_C D-H Without Acceptor       N4     -   H42    ...          ?
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          2

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          3
PLAT005_ALERT_5_G No _iucr_refine_instructions_details in CIF ....          ?
PLAT042_ALERT_1_G Calc. and Reported MoietyFormula Strings  Differ          ?
PLAT045_ALERT_1_G Calculated and Reported Z Differ by ............       0.50 Ratio
PLAT128_ALERT_4_G Alternate Setting of Space-group P21/c   .......      P21/n
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported   _diffrn_ambient_temperature        293 K
PLAT232_ALERT_2_G Hirshfeld Test Diff (M-X)  Cu1    --  N5      ..        9.9 su
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          2

   0 ALERT level A = Most likely a serious problem - resolve or explain
   2 ALERT level B = A potentially serious problem, consider carefully
   2 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   9 ALERT level G = General information/check it is not something unexpected

   4 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   5 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

Comment top

2-Benzoylpyridine semicarbazone (de Lima et al., 2008) is a Schiff base that is capable of N,N',O-chelation to transition metal ions. This feature has been documented in a copper(II) dichloride adduct in which the Schiff base exists as a neutral molecule (Peŕez-Rebolledo et al., 2006). However, the Cu^II atom in the title compound [Cu(NCO)(C₁₃H₁₁N₄O)] (Scheme I) is N,N',O-chelated by the mono-deprotonated Schiff base ligand and it is also covalently bonded to the nitrogen end of the cyanate ion. The metal center shows square-planar coordination that is distorted towards square-pyramidal coordination owing to an intermolecular Cu···N_cyanate interaction [2.623 (2) Å], which generates a centrosymmetric dimer (Fig. 1). The geometry is better interpreted as square planar as the Cu···N_cyanate···Cu angle is too acute [93.0 (1)°].

Adjacent dimers are linked by an amine N—H···N hydrogen-bond pair (Table 1), also giving a centrosymmetric cyclic association [graph set R²₂(8) (Etter et al., 1990], generating a linear chain parallel to [1 1 0].

Related literature top

For the synthesis of the Schiff base, see: de Lima et al. (2008). For a related copper(II) derivative, see: Peŕez-Rebolledo et al. (2006). For graph-set notation, see: Etter et al. (1990).

Experimental top

A methanol solution (20 ml) of 2-benzoylpyridine semicarbazone (0.240 g, 1 mmol) (de Lima et al., 2008), copper sulfate pentahydrate (0.249 g, 1 mmol) and sodium cyanate (0.065 g, 1 mmol) was heated for 5 h. The dark green solid was collected and recrystallized from methanol.

Computing details top

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

Fig. 1. Thermal ellipsoid plot (Barbour, 2001) of two molecules of [Cu(NCO)(C₁₃H₁₁N₄O)] that are linked by Cu···N_cyanate interactions (dashed bonds), at the 50% probability level. Hydrogen atoms are drawn as spheres of arbitrary radius.

(Cyanato-κN){1-[(E)-phenyl(pyridin-2-yl- κN)methylidene]semicarbazidato-κ²N¹,O}copper(II) top

Crystal data top

[Cu(C₁₃H₁₁N₄O)(NCO)]	F(000) = 700
M_r = 344.82	D_x = 1.709 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 838 reflections
a = 8.7601 (1) Å	θ = 2.4–28.3°
b = 7.6732 (1) Å	µ = 1.64 mm⁻¹
c = 20.0819 (3) Å	T = 293 K
β = 96.7467 (7)°	Prism, dark green
V = 1340.52 (3) Å³	0.30 × 0.25 × 0.20 mm
Z = 4

Data collection top

Bruker Kappa APEXII diffractometer	3069 independent reflections
Radiation source: fine-focus sealed tube	2728 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.031
ω scans	θ_max = 27.5°, θ_min = 2.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −10→11
T_min = 0.638, T_max = 0.735	k = −9→9
11886 measured reflections	l = −26→26

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.029	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.093	w = 1/[σ²(F_o²) + (0.0579P)² + 0.5121P] where P = (F_o² + 2F_c²)/3
S = 1.03	(Δ/σ)_max = 0.001
3069 reflections	Δρ_max = 0.37 e Å⁻³
208 parameters	Δρ_min = −0.47 e Å⁻³
2 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0221 (17)

Crystal data top

[Cu(C₁₃H₁₁N₄O)(NCO)]	V = 1340.52 (3) Å³
M_r = 344.82	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 8.7601 (1) Å	µ = 1.64 mm⁻¹
b = 7.6732 (1) Å	T = 293 K
c = 20.0819 (3) Å	0.30 × 0.25 × 0.20 mm
β = 96.7467 (7)°

Data collection top

Bruker Kappa APEXII diffractometer	3069 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	2728 reflections with I > 2σ(I)
T_min = 0.638, T_max = 0.735	R_int = 0.031
11886 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.029	2 restraints
wR(F²) = 0.093	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	Δρ_max = 0.37 e Å⁻³
3069 reflections	Δρ_min = −0.47 e Å⁻³
208 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cu1	0.31070 (2)	0.50325 (3)	0.506177 (10)	0.03203 (12)
O1	0.28257 (17)	0.3049 (2)	0.56285 (6)	0.0473 (4)
O2	0.5831 (2)	0.6387 (3)	0.67349 (8)	0.0696 (6)
N1	0.26412 (17)	0.6848 (2)	0.43675 (7)	0.0323 (3)
N2	0.13987 (16)	0.38948 (19)	0.45304 (7)	0.0287 (3)
N3	0.09476 (17)	0.2331 (2)	0.47511 (7)	0.0332 (3)
N4	0.1503 (3)	0.0571 (3)	0.56674 (9)	0.0526 (5)
H41	0.078 (2)	−0.018 (3)	0.5525 (15)	0.057 (8)*
H42	0.196 (3)	0.034 (4)	0.6065 (8)	0.059 (8)*
N5	0.47729 (18)	0.6213 (2)	0.56268 (8)	0.0391 (4)
C1	0.3226 (2)	0.8437 (3)	0.43590 (10)	0.0425 (4)
H1	0.3972	0.8773	0.4703	0.051*
C2	0.2763 (3)	0.9611 (3)	0.38550 (13)	0.0480 (5)
H2	0.3178	1.0727	0.3862	0.058*
C3	0.1682 (2)	0.9104 (3)	0.33440 (11)	0.0448 (5)
H3	0.1354	0.9875	0.2999	0.054*
C4	0.1084 (2)	0.7441 (3)	0.33435 (9)	0.0383 (4)
H4	0.0364	0.7071	0.2995	0.046*
C5	0.15699 (19)	0.6327 (2)	0.38691 (8)	0.0299 (3)
C6	0.09472 (19)	0.4563 (3)	0.39498 (8)	0.0289 (3)
C7	−0.00451 (19)	0.3697 (2)	0.34034 (8)	0.0295 (3)
C8	0.0435 (2)	0.3596 (3)	0.27703 (9)	0.0373 (4)
H8	0.1360	0.4106	0.2691	0.045*
C9	−0.0453 (2)	0.2744 (3)	0.22558 (9)	0.0438 (5)
H9	−0.0119	0.2674	0.1834	0.053*
C10	−0.1826 (2)	0.2003 (3)	0.23667 (10)	0.0453 (5)
H10	−0.2419	0.1424	0.2021	0.054*
C11	−0.2324 (2)	0.2114 (3)	0.29881 (11)	0.0438 (5)
H11	−0.3263	0.1626	0.3060	0.053*
C12	−0.1440 (2)	0.2947 (3)	0.35081 (9)	0.0351 (4)
H12	−0.1779	0.3006	0.3929	0.042*
C13	0.1784 (2)	0.2042 (3)	0.53522 (8)	0.0369 (4)
C14	0.5253 (2)	0.6252 (3)	0.61718 (10)	0.0396 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cu1	0.03601 (17)	0.03610 (18)	0.02273 (15)	−0.00921 (8)	−0.00184 (10)	−0.00184 (7)
O1	0.0603 (9)	0.0532 (9)	0.0253 (6)	−0.0211 (7)	−0.0086 (6)	0.0083 (6)
O2	0.0639 (10)	0.1105 (17)	0.0313 (7)	−0.0030 (10)	−0.0079 (7)	−0.0060 (9)
N1	0.0361 (7)	0.0323 (8)	0.0282 (7)	−0.0055 (6)	0.0017 (6)	−0.0025 (6)
N2	0.0310 (7)	0.0321 (7)	0.0227 (6)	−0.0053 (6)	0.0020 (5)	−0.0012 (5)
N3	0.0399 (7)	0.0341 (8)	0.0250 (6)	−0.0089 (6)	0.0013 (6)	0.0017 (6)
N4	0.0713 (13)	0.0508 (11)	0.0329 (9)	−0.0212 (10)	−0.0060 (8)	0.0121 (8)
N5	0.0370 (8)	0.0480 (10)	0.0316 (8)	−0.0072 (7)	0.0011 (6)	−0.0007 (7)
C1	0.0503 (11)	0.0374 (10)	0.0396 (10)	−0.0124 (8)	0.0041 (8)	−0.0064 (8)
C2	0.0609 (13)	0.0314 (9)	0.0536 (13)	−0.0093 (10)	0.0149 (10)	0.0014 (9)
C3	0.0528 (11)	0.0375 (11)	0.0452 (11)	0.0039 (9)	0.0104 (9)	0.0092 (9)
C4	0.0400 (9)	0.0381 (10)	0.0358 (9)	0.0018 (8)	−0.0002 (7)	0.0037 (8)
C5	0.0295 (7)	0.0314 (9)	0.0288 (7)	−0.0007 (6)	0.0034 (6)	−0.0017 (6)
C6	0.0270 (7)	0.0332 (8)	0.0261 (8)	−0.0013 (7)	0.0014 (6)	−0.0013 (7)
C7	0.0296 (7)	0.0297 (8)	0.0273 (7)	−0.0003 (6)	−0.0041 (6)	0.0010 (6)
C8	0.0344 (9)	0.0473 (11)	0.0295 (8)	−0.0053 (8)	0.0008 (7)	−0.0012 (8)
C9	0.0500 (11)	0.0512 (12)	0.0285 (8)	0.0002 (9)	−0.0031 (8)	−0.0051 (8)
C10	0.0465 (11)	0.0454 (12)	0.0396 (10)	−0.0040 (9)	−0.0142 (8)	−0.0070 (8)
C11	0.0317 (9)	0.0455 (11)	0.0515 (11)	−0.0083 (8)	−0.0062 (8)	0.0002 (9)
C12	0.0309 (8)	0.0368 (10)	0.0368 (9)	−0.0022 (7)	0.0013 (7)	0.0002 (7)
C13	0.0456 (10)	0.0403 (10)	0.0247 (8)	−0.0078 (8)	0.0039 (7)	0.0023 (7)
C14	0.0350 (9)	0.0442 (11)	0.0398 (10)	−0.0061 (8)	0.0060 (7)	−0.0032 (8)

Geometric parameters (Å, º) top

Cu1—O1	1.9335 (14)	C2—H2	0.9300
Cu1—N2	1.9404 (14)	C3—C4	1.379 (3)
Cu1—N5	1.9618 (16)	C3—H3	0.9300
Cu1—N1	1.9790 (15)	C4—C5	1.385 (2)
Cu1—N5ⁱ	2.6225 (17)	C4—H4	0.9300
O1—C13	1.272 (2)	C5—C6	1.475 (2)
O2—C14	1.188 (2)	C6—C7	1.475 (2)
N1—C1	1.324 (2)	C7—C8	1.388 (2)
N1—C5	1.349 (2)	C7—C12	1.388 (2)
N2—C6	1.293 (2)	C8—C9	1.382 (3)
N2—N3	1.354 (2)	C8—H8	0.9300
N3—C13	1.355 (2)	C9—C10	1.372 (3)
N4—C13	1.331 (3)	C9—H9	0.9300
N4—H41	0.876 (10)	C10—C11	1.372 (3)
N4—H42	0.869 (10)	C10—H10	0.9300
N5—C14	1.126 (2)	C11—C12	1.382 (3)
C1—C2	1.380 (3)	C11—H11	0.9300
C1—H1	0.9300	C12—H12	0.9300
C2—C3	1.368 (3)

O1—Cu1—N2	79.99 (6)	C3—C4—C5	119.16 (18)
O1—Cu1—N5	99.25 (6)	C3—C4—H4	120.4
N2—Cu1—N5	177.52 (6)	C5—C4—H4	120.4
O1—Cu1—N1	159.83 (6)	N1—C5—C4	120.48 (17)
N2—Cu1—N1	81.22 (6)	N1—C5—C6	115.08 (15)
N5—Cu1—N1	99.23 (7)	C4—C5—C6	124.40 (16)
O1—Cu1—N5ⁱ	99.82 (6)	N2—C6—C7	125.67 (17)
N2—Cu1—N5ⁱ	95.41 (6)	N2—C6—C5	112.66 (15)
N5—Cu1—N5ⁱ	87.05 (6)	C7—C6—C5	121.65 (15)
N1—Cu1—N5ⁱ	89.15 (6)	C8—C7—C12	118.85 (16)
C13—O1—Cu1	110.84 (11)	C8—C7—C6	119.40 (16)
C1—N1—C5	119.97 (16)	C12—C7—C6	121.74 (16)
C1—N1—Cu1	127.54 (13)	C9—C8—C7	120.43 (18)
C5—N1—Cu1	112.47 (12)	C9—C8—H8	119.8
C6—N2—N3	125.23 (14)	C7—C8—H8	119.8
C6—N2—Cu1	116.88 (12)	C10—C9—C8	120.13 (19)
N3—N2—Cu1	117.03 (10)	C10—C9—H9	119.9
N2—N3—C13	106.76 (14)	C8—C9—H9	119.9
C13—N4—H41	124 (2)	C9—C10—C11	120.02 (17)
C13—N4—H42	121 (2)	C9—C10—H10	120.0
H41—N4—H42	114 (3)	C11—C10—H10	120.0
C14—N5—Cu1	137.89 (16)	C10—C11—C12	120.38 (18)
N1—C1—C2	121.99 (19)	C10—C11—H11	119.8
N1—C1—H1	119.0	C12—C11—H11	119.8
C2—C1—H1	119.0	C11—C12—C7	120.18 (18)
C3—C2—C1	118.8 (2)	C11—C12—H12	119.9
C3—C2—H2	120.6	C7—C12—H12	119.9
C1—C2—H2	120.6	O1—C13—N4	118.09 (17)
C2—C3—C4	119.53 (19)	O1—C13—N3	125.08 (17)
C2—C3—H3	120.2	N4—C13—N3	116.82 (17)
C4—C3—H3	120.2	N5—C14—O2	175.1 (2)

N2—Cu1—O1—C13	3.55 (14)	Cu1—N1—C5—C4	179.09 (14)
N5—Cu1—O1—C13	−178.85 (14)	C1—N1—C5—C6	−177.08 (16)
N1—Cu1—O1—C13	25.1 (3)	Cu1—N1—C5—C6	1.45 (19)
N5ⁱ—Cu1—O1—C13	−90.27 (14)	C3—C4—C5—N1	−1.5 (3)
O1—Cu1—N1—C1	150.16 (19)	C3—C4—C5—C6	175.87 (18)
N2—Cu1—N1—C1	171.58 (18)	N3—N2—C6—C7	−4.9 (3)
N5—Cu1—N1—C1	−5.94 (18)	Cu1—N2—C6—C7	164.10 (13)
N5ⁱ—Cu1—N1—C1	−92.81 (17)	N3—N2—C6—C5	176.72 (15)
O1—Cu1—N1—C5	−28.2 (3)	Cu1—N2—C6—C5	−14.28 (19)
N2—Cu1—N1—C5	−6.80 (12)	N1—C5—C6—N2	8.2 (2)
N5—Cu1—N1—C5	175.67 (12)	C4—C5—C6—N2	−169.37 (17)
N5ⁱ—Cu1—N1—C5	88.80 (12)	N1—C5—C6—C7	−170.28 (15)
O1—Cu1—N2—C6	−175.17 (14)	C4—C5—C6—C7	12.2 (3)
N1—Cu1—N2—C6	12.18 (13)	N2—C6—C7—C8	−126.9 (2)
N5ⁱ—Cu1—N2—C6	−76.12 (14)	C5—C6—C7—C8	51.4 (2)
O1—Cu1—N2—N3	−5.25 (12)	N2—C6—C7—C12	51.9 (3)
N1—Cu1—N2—N3	−177.90 (13)	C5—C6—C7—C12	−129.86 (18)
N5ⁱ—Cu1—N2—N3	93.80 (12)	C12—C7—C8—C9	−0.8 (3)
C6—N2—N3—C13	174.42 (17)	C6—C7—C8—C9	178.00 (19)
Cu1—N2—N3—C13	5.43 (18)	C7—C8—C9—C10	0.5 (3)
O1—Cu1—N5—C14	−22.4 (3)	C8—C9—C10—C11	0.4 (3)
N1—Cu1—N5—C14	149.4 (2)	C9—C10—C11—C12	−1.0 (3)
N5ⁱ—Cu1—N5—C14	−121.9 (3)	C10—C11—C12—C7	0.8 (3)
C5—N1—C1—C2	0.7 (3)	C8—C7—C12—C11	0.2 (3)
Cu1—N1—C1—C2	−177.57 (16)	C6—C7—C12—C11	−178.62 (18)
N1—C1—C2—C3	−1.0 (3)	Cu1—O1—C13—N4	176.97 (17)
C1—C2—C3—C4	0.0 (3)	Cu1—O1—C13—N3	−1.7 (3)
C2—C3—C4—C5	1.3 (3)	N2—N3—C13—O1	−2.4 (3)
C1—N1—C5—C4	0.6 (3)	N2—N3—C13—N4	178.93 (19)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H41···N3ⁱⁱ	0.88 (1)	2.27 (1)	3.139 (2)	173 (3)

Symmetry code: (ii) −x, −y, −z+1.

Experimental details

Crystal data
Chemical formula	[Cu(C₁₃H₁₁N₄O)(NCO)]
M_r	344.82
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	8.7601 (1), 7.6732 (1), 20.0819 (3)
β (°)	96.7467 (7)
V (Å³)	1340.52 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	1.64
Crystal size (mm)	0.30 × 0.25 × 0.20

Data collection
Diffractometer	Bruker Kappa APEXII diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.638, 0.735
No. of measured, independent and observed [I > 2σ(I)] reflections	11886, 3069, 2728
R_int	0.031
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.029, 0.093, 1.03
No. of reflections	3069
No. of parameters	208
No. of restraints	2
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.37, −0.47

Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), X-SEED (Barbour, 2001), publCIF (Westrip, 2010).